Simply is not the right word. The bodies will be flying at them with high velocity and smack them in the face. In order to get inside the HK's have to jump, step, swing whatever - all those movements include detaching their magnetic boots, even just one. With nothing to hold onto the winds will push them back, they are simply too powerful. Even with a jetpack they wouldn't get in. They can't cancel the windows from closing if they are not inside. Its simply impossible.
The HK's could simply push the bodies away and move through them with the magnetic boots. Then stand on the ceiling until the shields go down. Or cancel the shields from even coming back online with the console.
Not Jedi, biologicals. They are trained to kill biologicals, the Force puts a spanner in the works, there are no defenses that are specifically effective against Force users. They have an edge in just about anything. E.g. bomb explosions they can shield against, same with flamethrowers and carbonite attacks, they can push toxins out of their bodies, they can deflect turret fire etc. And sure, they have a factory, but I don't think production is anywhere near that fast. Eventually, superior numbers will prevail. Let's also remember that if the invasion of Malachor fails he lost what, 100 units? And has 0 time to build more.
With the invasion the HK's are programmed to kill Jedi, and the defenses of the factory are programmed to also kill Jedi. The Sith would be slaughtered. the HK's could also use flamethrowers and carbonite attacks to kill the Sith. Or they could be suicide bombers and run with bombs about to go. Droids can be programmed to do anything.
EDIT: with the factory, new droids are constantly being produced. The numbers argument is sort of, not completely, but sort of invalid.